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Oncopeltus fasciatus genome annotations v0.5.3
,The Oncopeltus fasciatus genome was recently sequenced and annotated as part of the i5k pilot project by the Baylor College of Medicine. The O. fasciatus research community has manually reviewed and curated the computational gene predictions and generated an official gene set, OGSv1.1.,Oncopeltus fasciatus has been an established lab organism for over 60 years, and has been used for a wide range of studies from physiology to development and evolution. As a relatively conservative and generalized species, it affords a baseline against which other species can be compared.,For example, this species has the same piercing and sucking type mouthparts as its less benign relatives, including the blood-sucking kissing bug, Rhodnius prolixus, and the brown marmorated stink bug, Halyomorpha halys, which are disease vector and agricultural pest species, respectively. Unlike the pest species, the benign, seed-feeding Oncopeltus can be functionally investigated in the lab by RNA interference (RNAi). Comparing the genomes, and conducting experimental lab work in Oncopeltus, will help to identify unique features of the pest species, and thus inform management strategies for them.,More generally, Oncopeltus is a key species for comparisons across the insects. It is one of the few experimentally tractable hemimetabolous species that can ground comparisons with the completely metamorphosing species of the Holometabola (e.g., flies, beetles, wasps). Topics investigated in this framework include reproductive biology and development of the legs, wings, body segments, extraembryonic membranes, and overall establishment of the body plan.,This dataset presents the Oncopeltus fasciatus gene set BCM_v_0.5.3, which was generated computationally. RNA-Seq data was used with additional protein homology data for a MAKER automated annotation of the Oncopeltus fasciatus genome assembly 1.0. Further annotation method details will be available in a forthcoming publication.,NOTE: This gene set is an unstable pre-release (v0.5.3), and was provided to facilitate manual curation and analyses before the official gene set is released. Gene identifiers from this gene set will likely not be maintained.,If you wish to use this dataset, please follow the Baylor College of Medicine's conditions for data use: https://www.hgsc.bcm.edu/bcm-hgsc-conditions-use,
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Leptinotarsa decemlineata genome annotations v0.5.3
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,The Leptinotarsa decemlineata genome was recently sequenced and annotated as part of the i5k pilot project by the Baylor College of Medicine. This dataset presents the Leptinotarsa decemlineata gene set BCM_v_0.5.3, which was generated computationally. RNA-Seq data was used with additional protein homology data for a MAKER automated annotation of the Leptinotarsa decemlineata genome assembly 1.0. Further annotation method details will be available in a forthcoming publication.,NOTE: This gene set is an unstable pre-release (v0.5.3), and was provided to facilitate manual curation and analyses before the official gene set is released. Gene identifiers from this gene set will likely not be maintained.,If you wish to use this dataset, please follow the Baylor College of Medicine's conditions for data use: https://www.hgsc.bcm.edu/bcm-hgsc-conditions-use,
Leptinotarsa decemlineata genome assembly 1.0
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,The Baylor College of Medicine recently sequenced and annotated the Leptinotarsa decemlineata genome as part of the i5k pilot project. This dataset presents the Leptinotarsa decemlineata genome v1.0. This assembly version is the pre-release version, prior to filtering and quality control by the National Center for Biotechnology Information's GenBank resource. Assembly method details will be available in a forthcoming publication.,The Colorado potato beetle is considered the economically most significant defoliator of potato in northern latitudes worldwide. The range of this insect is continuing to expand, and it is likely to eventually colonize all potato-producing areas with temperate climate. Within it's native habitat, the beetle feeds on native solanaceous plants, S. angustifolium, S. elaeagnifolium, and buffalo bur, S. rostratum. However, it has adapted to potatoes and other solanaceous crops after its range expansion.,Due to the lack of any natural enemies that have been able to evolve seasonal adaptations, the cornerstone of Colorado potato beetle management has been the use of insecticides. However, the beetle has shown a remarkable ability to develop resistance to most insecticides used for its control. The mechanism(s) of insecticide resistance is yet unknown and genomic sequencing will lead to major advances in managing this pest in commercial plant production.,If you wish to use this dataset, please follow the Baylor College of Medicine's conditions for data use: https://www.hgsc.bcm.edu/bcm-hgsc-conditions-use,
Hyalella azteca Official Gene Set v1.0
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,The Hyalella azteca genome was recently sequenced and annotated as part of the i5k pilot project by the Baylor College of Medicine. The Hyalella azteca research community has manually reviewed and curated the computational gene predictions and generated an official gene set, OGSv1.0. The OGS is an integration of automatic gene predictions from Maker with manual annotations by the research community (via the Apollo manual annotation software).,If you wish to use this dataset, please follow the Baylor College of Medicine's conditions for data use: https://www.hgsc.bcm.edu/bcm-hgsc-conditions-use,
In-house annotated gene set for the pecan weevil, Curculio caryae
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,This in-house annotated gene set was created using the following methods.,RNA was isolated from the head and thorax segments of one adult male and one adult female pecan weevil using the NucleoMag RNA Kit (Macherey-Nagel, Düren, Germany, 744350.1) according to kit protocols. Isolated RNA was processed into PacBio Kinnex sequencing libraries using the Iso-Seq express 2.0 kit (Pacific Biosciences, Menlo Park, CA, USA 103-071-500) and Kinnex full-length RNA kit (Pacific Biosciences, Menlo Park, CA, USA,103-072-000). The prepared library was bound and sequenced at the USDA-ARS Veterinary Pest Genetics Research Unit in Kerrville, Texas, on two Pacific Biosciences SMRT cell trays with a Revio system (Pacific Biosciences, Menlo Park, CA, USA, 102-202-200) beginning with a 2-h pre-extension followed by a 30-h movie collection time. After sequencing, circular consensus sequences from the PacBio Sequel Revio subreads were obtained using the SMRTLink v13.0 software. Reads were subsequently mapped to the repeat-masked genome assembly using minimap2 with arguments for spliced nucleotide sequences (-ax splice:hq) to generate sam mapping files. These were then compressed into bam files using samtools view -bS and used as input for gene model prediction with the Braker version 3.0.8 program (https://github.com/Gaius-Augustus/BRAKER), generating 72,879 gene models. These gene models and amino acid protein predictions were further curated and annotated with gene ontologies and protein domains using InterProScan-5.73-104.0 with PANTHER-19.0 and Pfam-37.2 databases (https://github.com/ebi-pf-team/interproscan), resulting in 19,508 InterProScan results.,
Genbank Accession Numbers for DNA Sequences Amplified from a Subset of Environmental Samplers 2016 - 2017
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These data contain Genbank Accession numbers for DNA amplified and sequenced from a subset of Environmental Samplers that were positive for Ceratocystis lukuohia and Austropuccinia by quantitative PCR (qPCR)
Genbank Accession Numbers for DNA Sequences Amplified from a Subset of Environmental Samplers 2016 - 2017
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These data contain Genbank Accession numbers for DNA amplified and sequenced from a subset of Environmental Samplers that were positive for Ceratocystis lukuohia and Austropuccinia by quantitative PCR (qPCR)
Amplicon sequencing of pollen foraged by Bombus affinis for compositional analysis
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This study generated genetic 'barcode' data using high-throughput sequencing to characterize pollen collected by the endangered rusty-patched bumblebee, Bombus affinis. Pollen samples were associated with a single Bombus affinis colony within a structure in Red Wing, Minnesota, USA, as previously described by Boone et al. (2022). This data release consists of two tab-delimited files: 1) sample.metadata.txt includes sample identifiers and accessions assigned by the National Center for Biotechnology Information (NCBI), the authoritative repository for publicly funded genetic data in the United States. These accessions can be used individually to obtain raw sequencing data or sample information at www.ncbi.nih.nlm.gov. Alternatively, the BioProject accession PRJNA1045705 can be searched to retrieve the full set of data and sample accessions listed in the file. Entity and attribute metadata are provided for this file. 2) taxon.counts.txt includes the inferred counts, or number of sequences, attributable to each identified taxon in each sample. Taxa are in rows and sequencing libraries are in columns. Taxa are listed by scientific name and the taxonomic rank of that scientific name. A numeric taxonomic identifier used by NCBI for each taxon is also provided, as the taxonomic identifier is unique in the NCBI databases whereas scientific names may not be. Entity and attribute data are not provided for this file due to its size and repetitive content.
Voucher and metagenetic sequencing of DNA barcodes of wild-collected bees (Apoidea) from Iowa, USA
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High-throughput methods for identification of pollinator taxa are desirable to improve our understanding of pollinator distributions, population trends, and ecology. Genetic sequencing of taxonomically informative 'barcode' loci is one high-throughput strategy, which can be applied to individual specimens using Sanger technology and to complex mixtures using metabarcoding technology. This study generated Sanger sequencing data from morphologically identified specimens and metabarcoding data derived from pooled tissues. This data release consists of several files: 1. sample.metadata.txt, which contains sampling metadata and identifiers linking to sequence data that has been deposited in the Sequence Read Archive of the National Center for Biotechnology Information (NCBI). This database is authoritative and comprehensive for sharing high-throughput sequence data produced with public funds. All NCBI-derived accessions listed in the file can be searched at www.ncbi.nlm.nih.gov to retrieve sample and sequence information 2. raw.counts.txt, which is a tab-delimited table of counts of individual metabarcode sequences that are attributed to each detected bee genus. 3. BeeSangerSequencesFASTA.txt, which is a text document in FASTA format containing the DNA sequences obtained from the individual specimens using Sanger sequencing technology. 4. reference.sequences.fasta, which is a text document in FASTA format containing the DNA sequences obtained from public databases for taxonomic assignment of metabarcode sequences as described in the process steps.